CNV observed in this study											"CNV observed by Graubert et al. PLoS Genet 2007, 3:e3"						
Strain	Region	Type	Chromosome	Start	End	Copy #	StdDev	Included	Excluded	%Included	Chr	Start	Stop	A/J	129X1/SvJ	BALB/cByJ	Match between this study and Graubert et al 2007
129P3/J	1	AMPLIFICATION	1	11836452	11836452	0.92	0	1	0	100							
Balb/cJ	2	AMPLIFICATION	3	34573648	35036992	0.59	0.24	5	0	100							
129P3/J	3	DELETION	4	41866402	43040347	-0.36	0.2	12	0	100							
Balb/cJ	3	DELETION	4	41902351	42707295	-0.93	0.12	9	0	100							
Balb/cJ	4	DELETION	4	59941391	60844847	-1.16	0.22	6	0	100	4	59951474	61020903	-0.46	-0.15	-0.04	No
Balb/cJ	5	DELETION	4	60923153	61210925	-0.46	0.21	4	0	100							
Balb/cJ	6	DELETION	4	111026380	112711420	-0.73	0.33	12	0	100							
129P3/J	6	DELETION	4	111070933	112556265	-0.48	0.12	10	0	100							
Balb/cJ	7	DELETION	4	120706328	121596601	-0.93	0.35	8	1	88.89	4	120748705	121521377	-0.20	-0.25	-1.54	Yes
Balb/cJ	8	DELETION	5	10962257	11414510	-1.16	0.1	6	0	100	5	10895827	11348377	-0.07	-0.17	-0.1	No
129P3/J	9	AMPLIFICATION	5	14355728	14449485	0.49	0.09	7	0	100	5	14286036	14539614	0.9	0.26	0.52	Yes
Balb/cJ	9	AMPLIFICATION	5	14355728	14449485	0.59	0.1	7	0	100	5	14286036	14539614	0.9	0.26	0.52	Yes
129P3/J	10	DELETION	5	74949452	75222505	-1.09	0.2	6	0	100							
Balb/cJ	10	DELETION	5	74949452	75016150	-0.73	0.09	4	0	100							
129P3/J	11	DELETION	5	92657945	92687880	-0.48	0.11	2	0	100							
Balb/cJ	12	DELETION	5	92687880	94858582	-0.73	0.21	16	3	84.21							
129P3/J	12	DELETION	5	92743002	94858582	-1.09	0.21	14	4	77.78	5	92745349	94363178	0	-0.7	-0.65	Yes
Balb/cJ	13	AMPLIFICATION	7	6831956	8440623	0.32	0.13	15	0	100							
129P3/J	14	DELETION	7	16822989	18504465	-1.09	0.28	12	1	92.31	7	16787962	18664180	-0.13	-0.77	-0.51	Yes
Balb/cJ	14	DELETION	7	16822989	18504465	-1.75	0.54	12	1	92.31	7	16787962	18664180	-0.13	-0.77	-0.51	Yes
Balb/cJ	15	DELETION	7	26661184	28741939	-0.46	0.15	17	0	100	7	26863102	28865264	-0.26	-0.34	-0.39	Yes
129P3/J	15	DELETION	7	26838454	28615398	-0.61	0.11	15	0	100	7	26863102	28865264	-0.26	-0.34	-0.39	Yes
129P3/J	16	AMPLIFICATION	8	19587365	19868412	0.49	0.23	3	0	100							
129P3/J	17	DELETION	8	20065625	20483927	-0.48	0.24	6	0	100	8	20052472	20446569	-0.50	-0.50	-0.85	Yes
Balb/cJ	17	DELETION	8	20065625	20409101	-0.62	0.12	3	0	100	8	20052472	20446569	-0.50	-0.50	-0.85	Yes
129P3/J	18	AMPLIFICATION	8	68650251	68666719	0.64	0.1	2	0	100							
129P3/J	19	AMPLIFICATION	9	46952956	47225039	0.64	0.2	4	0	100							
129P3/J	20	AMPLIFICATION	9	124004054	124006210	0.64	0.06	2	0	100							
Balb/cJ	21	AMPLIFICATION	12	108934014	111152622	0.32	0.16	12	0	100	12	109111835	109238974	0.74	0.22	0.62	Yes
129P3/J	22	AMPLIFICATION	12	111187360	111634638	0.78	0.01	2	0	100							
Balb/cJ	22	AMPLIFICATION	12	111187360	111634638	0.77	0.05	2	0	100							
129P3/J	23	AMPLIFICATION	13	62936479	63343872	0.49	0.16	7	0	100	13	62741232	63470597	0.91	0.29	0.59	Yes
Balb/cJ	23	AMPLIFICATION	13	62936479	63343872	0.77	0.13	7	0	100	13	62741232	63470597	0.91	0.29	0.59	Yes
129P3/J	24	AMPLIFICATION	14	3080384	5405067	0.92	0.26	11	1	91.67							
Balb/cJ	25	AMPLIFICATION	17	6068506	6273514	0.59	0.14	4	0	100							
129P3/J	26	AMPLIFICATION	17	28309463	28687067	0.64	0.05	3	0	100	17	28262079	28735845	0.54	0.03	0.95	No
Balb/cJ	27	DELETION	17	57288113	57288113	-1.16	0	1	0	100							
Balb/cJ	28	AMPLIFICATION	X	3084190	3626369	0.32	0.06	9	1	90							
Balb/cJ	29	DELETION	X	141242821	143555236	-0.46	0.27	17	1	94.44